Downloading the Gene level Copy number files from TCGA, I computed CIN in the following way: - gene CNV > 2.25 = Amp - gene CNV < 1.75 = Del
I have mapped cytobands to gene entrez ids using org.Hs.egMAP and using the cytobands I extract the gene level CIN which will be added at cytoband level for all the genes in that cytoband across all the different cases that we have from TCGA-SARC
Plots: 1- Overall boxplots: for each chromosome all the cytoband CIN per sarcoma type
1b - Overall heatmap: for each chromosome a heatmap with all the CIN per cytobands and annotation on the side for each sarcoma type
2- HRD boxplots: The same as before but separating HRDhigh/low
2b - is there any cytoband differentially expressed between HRD/low groups in particular?
3- Make enrichment in those cytobands :)